3M79

A tetrameric Zn-bound cytochrome cb562 complex with covalently and non-covalently stabilized interfaces crystallized in the presence of Cu(II) and Zn(II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IQ6 

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3647.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.547α = 90
b = 78.068β = 90
c = 178.339γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rVertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing)2010-01-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.0SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.09989.1793.60.10249.54927249272
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2184.20.1761.510.36358

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3IQ62.159.875273649203356693.30.230.2250.2220.271RANDOM27.461
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.04-0.050.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.287
r_dihedral_angle_3_deg16.866
r_dihedral_angle_4_deg16.043
r_dihedral_angle_1_deg6.068
r_scangle_it2.151
r_scbond_it1.475
r_angle_refined_deg1.095
r_mcangle_it0.798
r_mcbond_it0.44
r_nbtor_refined0.278
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.287
r_dihedral_angle_3_deg16.866
r_dihedral_angle_4_deg16.043
r_dihedral_angle_1_deg6.068
r_scangle_it2.151
r_scbond_it1.475
r_angle_refined_deg1.095
r_mcangle_it0.798
r_mcbond_it0.44
r_nbtor_refined0.278
r_symmetry_vdw_refined0.275
r_nbd_refined0.202
r_xyhbond_nbd_refined0.177
r_symmetry_hbond_refined0.12
r_metal_ion_refined0.09
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6544
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms352

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOLREPphasing